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Recent Clinical Sequencing Papers of Note: May 21, 2014


Somatic mutation load of estrogen receptor-positive breast tumors predicts overall survival: an analysis of genome sequence data.
Haricharan S, Bainbridge MN, Scheet P, Brown PH.
Breast Cancer Res Treat. 2014 May 18. [Epub ahead of print]

Inactivating mutation in the prostaglandin transporter gene, SLCO2A1, associated with familial digital clubbing, colon neoplasia, and NSAID resistance.
Guda K, Fink SP, Milne G, Molyneaux N, et al.
Cancer Prev Res. 2014 May 16. [Epub ahead of print]

Microsatellite genotyping reveals a signature in breast cancer exomes.
McIver LJ, Fonville NC, Karunasena E, Garner HR.
Breast Cancer Res Treat. 2014 May 17. [Epub ahead of print]

FBXW7 Mutations in melanoma and a new therapeutic paradigm.
Aydin IT, Melamed RD, Adams SJ, Castillo-Martin M, et al.
J Natl Cancer Inst. 2014 May 16;106(6).

De novo ANKRD11 and KDM1A gene mutations in a male with features of KBG syndrome and Kabuki syndrome.
Tunovic S, Barkovich J, Sherr EH, Slavotinek AM.
Am J Med Genet A. 2014 May 16. [Epub ahead of print]

Exosomes in human semen carry a distinctive repertoire of small non-coding RNAs with potential regulatory functions.
Vojtech L, Woo S, Hughes S, Levy C, et al.
Nucleic Acids Res. 2014 May 16. [Epub ahead of print]

Clinical validation of KRAS, BRAF, and EGFR mutation detection using next-generation sequencing.
Lin MT, Mosier SL, Thiess M, Beierl KF, et al.
Am J Clin Pathol. 2014 Jun;141(6):856-66.

Development and validation of a new HPV genotyping assay based on next-generation sequencing.
Yi X, Zou J, Xu J, Liu T, et al.
Am J Clin Pathol. 2014 Jun;141(6):796-804.

A unified test of linkage analysis and rare-variant association for analysis of pedigree sequence data.
Hu H, Roach JC, Coon H, Guthery SL, et al.
Nat Biotechnol. 2014 May 18. [Epub ahead of print]

Whole-exome sequencing and clinical interpretation of formalin-fixed, paraffin-embedded tumor samples to guide precision cancer medicine.
Van Allen EM, Wagle N, Stojanov P, Perrin DL, et al.
Nat Med. 2014 May 18. [Epub ahead of print]

Neu-Laxova syndrome, an inborn error of serine metabolism, is caused by mutations in PHGDH.
Shaheen R, Rahbeeni Z, Alhashem A, Faqeih E, et al.
Am J Hum Genet. 2014 May 14. [Epub ahead of print]

Mutational context and diverse clonal development in early and late bladder cancer.
Nordentoft I, Lamy P, Birkenkamp-Demtröder K, Shumansky K, et al.
Cell Rep. 2014 May 14. [Epub ahead of print]

Next-generation sequencing improves the diagnosis of thyroid FNA specimens with indeterminate cytology.
Le Mercier M, D'Haene N, De Nève N, Blanchard O, et al.
Histopathology. 2014 May 17. [Epub ahead of print]

Mutations in TJP2 cause progressive cholestatic liver disease.
Sambrotta M, Strautnieks S, Papouli E, Rushton P, et al.
Nat Genet. 2014 Apr;46(4):326-8.

Exome sequencing reveals a potential mutational trajectory and treatments for a specific pancreatic cancer patient.
Cotterell J.
Onco Targets Ther. 2014 May 3;7:655-62.

FaSD-somatic: A fast and accurate somatic SNV detection algorithm for cancer genome sequencing data.
Wang W, Wang P, Xu F, Luo R, et al.
Bioinformatics. 2014 May 14. [Epub ahead of print]

Rare variants in FBN1 and FBN2 are associated with severe adolescent idiopathic scoliosis.
Buchan JG, Alvarado DM, Haller GE, Cruchaga C, et al.
Hum Mol Genet. 2014 May 15. [Epub ahead of print]

Mutations in the cholesterol transporter gene ABCA5 are associated with excessive hair overgrowth.
DeStefano GM, Kurban M, Anyane-Yeboa K, Dall'Armi C, et al.
PLOS Genet. 2014 May 15;10(5):e1004333.

Acquired isochromosome 12p, somatic TP53 and PTEN mutations, and a germline ATM variant in an adolescent male with concurrent acute megakaryoblastic leukemia and mediastinal germ cell tumor.
Oshrine BR, Olsen MN, Heneghan M, Wertheim G, et al.
Cancer Genet. 2014 Apr 5. [Epub ahead of print]

A labor- and cost-effective non-optical semiconductor (Ion Torrent) next-generation sequencing of the SLC12A3 and CLCNKA/B genes in Gitelman's syndrome patients.
Tavira B, Gómez J, Santos F, Gil H, et al.
J Hum Genet. 2014 May 15. [Epub ahead of print]

The validation and clinical implementation of BRCAplus: a comprehensive high-risk breast cancer diagnostic assay.
Chong HK, Wang T, Lu HM, Seidler S, et al.
PLOS One. 2014 May 15;9(5):e97408.

Noninvasive prenatal testing for autosomal recessive conditions by maternal plasma sequencing in a case of congenital deafness.
Meng M, Li X, Ge H, Chen F, et al.
Genet Med. 2014 May 15. [Epub ahead of print]

Somatic retrotransposition in human cancer revealed by whole-genome and exome sequencing.
Helman E, Lawrence ML, Stewart C, Sougnez C, et al.
Genome Res. 2014 May 13. [Epub ahead of print]

Characterization of the genomic architecture and mutational spectrum of a small cell prostate carcinoma.
Scott AF, Mohr DW, Ling H, Scharpf RB, et al.
Genes. 2014 May 12;5(2):366-84.

Enriched variations in TEKT4 and breast cancer resistance to paclitaxel.
Jiang YZ, Yu KD, Peng WT, Di GH, et al.
Nat Commun. 2014 May 13;5:3802.

Autosomal dominant hypoparathyroidism caused by germline mutation in GNA11: phenotypic and molecular characterization.
Li D, Opas EE, Tuluc F, Metzger DL, et al.
J Clin Endocrinol Metab. 2014 May 13 [Epub ahead of print]

Germline and somatic DICER1 mutations in a pituitary blastoma causing infantile onset Cushing disease.
Sahakitrungruang T, Srichomthong C, Pornkunwilai S, Amornfa J, et al.
J Clin Endocrinol Metab. 2014 May 13 [Epub ahead of print]

Microbial profiling of combat wound infection through detection microarray and next-generation sequencing.
Be NA, Allen JE, Brown TS, Gardner SN, et al.
J Clin Microbiol. 2014 May 14. [Epub ahead of print]

Whole-exome sequencing and functional studies identify RPS29 as a novel gene mutated in multi-case Diamond-Blackfan anemia families.
Mirabello L, Macari ER, Jessop L, Ellis SR, et al.
Blood. 2014 May 14. [Epub ahead of print]

Reducing false positive incidental findings with ensemble genotyping and logistic regression-based variant filtering methods.
Hwang KB, Lee IH, Park JH, Hambuch T, et al.
Hum Mutat. 2014 May 14. [Epub ahead of print]

Autosomal dominant eccentric core disease caused by a heterozygous mutation in the MYH7 gene.
Romero NB, Xie T, Malfatti E, Schaeffer U, et al.
J Neurol Neurosurg Psychiatry. 2014 May 14. [Epub ahead of print]

Next-generation sequencing revealed a novel mutation in the gene encoding the beta subunit of rod phosphodiesterase.
Shen S, Sujirakul T, Tsang SH.
Ophthalmic Genet. 2014 May 14:1-9. [Epub ahead of print]

High-throughput mutation profiling improves diagnostic stratification of sporadic medullary thyroid carcinomas.
Simbolo M, Mian C, Barollo S, Fassan M, et al.
Virchows Arch. 2014 May 15. [Epub ahead of print]

A novel DFNA36 mutation in TMC1 orthologous to the Beethoven (Bth) mouse associated with autosomal dominant hearing loss in a Chinese family.
Zhao Y, Wang D, Zong L, Zhao F, et al.
PLOS One. 2014 May 14;9(5):e97064.

Novel CLN3 mutation causing autophagic vacuolar myopathy.
Cortese A, Tucci A, Piccolo G, Galimberti CA, et al.
Neurology. 2014 May 14. [Epub ahead of print]

VARS2 and TARS2 mutations in patients with mitochondrial encephalomyopathies.
Diodato D, Melchionda L, Haack T, Dallabona C, et al.
Hum Mutat. 2014 May 14. [Epub ahead of print]

A form of the metabolic syndrome associated with mutations in DYRK1B.
Keramati AR, Fathzadeh M, Go GW, Singh R, et al.
N Engl J Med. 2014 May 15;370(20):1909-19.

Integrated genomic sequencing reveals mutational landscape of T-cell prolymphocytic leukemia.
Kiel MJ, Velusamy T, Rolland D, Sahasrabuddhe AA, et al.
Blood. 2014 May 13. [Epub ahead of print]

Mutation analysis of seven known glaucoma-associated genes in Chinese patients with glaucoma.
Huang X, Li M, Guo X, Li S, et al.
Invest Ophthalmol Vis Sci. 2014 May 13. [Epub ahead of print]

Molecular profiling of appendiceal epithelial tumors using massively parallel sequencing to identify somatic mutations.
Liu X, Mody K, de Abreu FB, Pipas JM, et al.
Clin Chem. 2014 May 12. [Epub ahead of print]

Advanced bone age in a girl with Wiedemann-Steiner syndrome and an exonic deletion in KMT2A (MLL).
Mendelsohn BA, Pronold M, Long R, Smaoui N, Slavotinek AM.
Am J Med Genet A. 2014 May 12. [Epub ahead of print]

Diagnostic yield of clinical next-generation sequencing panels for epilepsy.
Wang J, Gotway G, Pascual JM, Park JY.
JAMA Neurol. 2014 May 1;71(5):650-1.

Applicability of next-generation sequencing to decalcified formalin-fixed and paraffin-embedded chronic myelomonocytic leukaemia samples.
Bernard V, Gebauer N, Dinh T, Stegemann J, et al.
Int J Clin Exp Pathol. 2014 Mar 15;7(4):1667-76.

RNA-seq reveals determinants of sensitivity to chemotherapy drugs in esophageal carcinoma cells.
Yang LX, Li BL, Liu XH, Yuan Y, et al.
Int J Clin Exp Pathol. 2014 Mar 15;7(4):1524-33.

Whole-exome sequencing identifies a novel genotype-phenotype correlation in the entactin domain of the known deafness gene TECTA.
Choi BY, Kim J, Chung J, Kim AR, et al.
PLOS One. 2014 May 9;9(5):e97040.

Recessive C10orf2 mutations in a family with infantile-onset spinocerebellar ataxia, sensorimotor polyneuropathy, and myopathy.
Park MH, Woo HM, Hong YB, Park JH, et al.
Neurogenetics. 2014 May 10. [Epub ahead of print]

Recurrent gain-of-function mutations of RHOA in diffuse-type gastric carcinoma.
Kakiuchi M, Nishizawa T, Ueda H, Gotoh K, et al.
Nat Genet. 2014 May 11. [Epub ahead of print]

Whole-genome sequencing and comprehensive molecular profiling identify new driver mutations in gastric cancer.
Wang K, Yuen ST, Xu J, Lee SP, et al.
Nat Genet. 2014 May 11. [Epub ahead of print]

Identification of two novel ATP6V0A2 mutations in an infant with cutis laxa by exome sequencing.
Ritelli M, Chiarelli N, Quinzani S, Dordoni C, et al.
J Dermatol Sci. 2014 Apr 18. [Epub ahead of print]

DEPDC5 mutations in families presenting as autosomal dominant nocturnal frontal lobe epilepsy.
Picard F, Makrythanasis P, Navarro V, Ishida S, et al.
Neurology. 2014 May 9. [Epub ahead of print]

Mutations in EMP2 cause childhood-onset nephrotic syndrome.
Gee HY, Ashraf S, Wan X, Vega-Warner V, et al.
Am J Hum Genet. 2014 May 7. [Epub ahead of print]

Return of genomic results to research participants: the floor, the ceiling, and the choices in between.
Jarvik GP, Amendola LM, Berg JS, Brothers K, et al.
Am J Hum Genet. 2014 May 7. [Epub ahead of print]

Determination of the allelic frequency in Smith-Lemli-Opitz syndrome by analysis of massively parallel sequencing data sets.
Cross JL, Iben J, Simpson C, Thurm A, et al.
Clin Genet. 2014 May 9. [Epub ahead of print]

Detection of gene rearrangements in targeted clinical next-generation sequencing.
Abel HJ, Al-Kateb H, Cottrell CE, Bredemeyer AJ, et al.
J Mol Diagn. 2014 May 6. [Epub ahead of print]

The Scan

Positive Framing of Genetic Studies Can Spark Mistrust Among Underrepresented Groups

Researchers in Human Genetics and Genomics Advances report that how researchers describe genomic studies may alienate potential participants.

Small Study of Gene Editing to Treat Sickle Cell Disease

In a Novartis-sponsored study in the New England Journal of Medicine, researchers found that a CRISPR-Cas9-based treatment targeting promoters of genes encoding fetal hemoglobin could reduce disease symptoms.

Gut Microbiome Changes Appear in Infants Before They Develop Eczema, Study Finds

Researchers report in mSystems that infants experienced an enrichment in Clostridium sensu stricto 1 and Finegoldia and a depletion of Bacteroides before developing eczema.

Acute Myeloid Leukemia Treatment Specificity Enhanced With Stem Cell Editing

A study in Nature suggests epitope editing in donor stem cells prior to bone marrow transplants can stave off toxicity when targeting acute myeloid leukemia with immunotherapy.